The Punctuated Evolution program can detect significant punctuated
molecular evolution from phylogenetic trees inferred from sequence data. Where
the punctuational effect is present the program will report the proportion of
evolution attributable to speciation events (nodes). It also reports the
deviation from the molecular clock caused by punctuational effects. (See papers
above for methodological details)

A recognised artifact of phylogeny
reconstruction known as
the node-density effect can mimic punctuational effects. However, the node
density artifact can be tested for statistically (See
papers above). If the
artifact is present the program reports it.

Input Tree
File

The input tree(s) should be in Nexus format

The trees should be fully bifurcating

Outgroup
and rooting

Trees must be inferred with an outgroup

Before analysis the trees must be rooted using the outgroup and the outgroup removed (see papers
above for a
detailed explanation of why this must be done).

The result and
output

The first table of the results provide
information about the input file

Tree file name

Number of tree in the Nexus file

Reference ID number

The second table shows the results of the test
for the punctuational effect

Number (and percent) of trees with a significant
β

Number (and percent) of trees with a significant
β and δ < 1

Conclusion (whether there is a significant
punctuational effect or node-density artifact is present of neither)

NB the output
is simple if a single tree is analyzed, however, see See papers above for how we determine the presents of the
punctuational effect and the node density artifact integrating over a Bayesian
sample of phylogenies.

The third table only appears if a significant
punctuational effect is detected - It shows

Percentage of evolution in the tree attributable
to punctuational effects

Punctuational
effects contribution of the deviation from molecular clock (r2)

NB again this
is simple if a single tree is analyzed. See papers
above for how we
integrate over a Bayesian sample.